samples_db

A <code>data.frame</code> of example IGH human naive b-cell repertiore data from five
individuals (see references). Overall, the data set includes 6 samples.
A single individual has two samples (Individual I5),
one is short read sequences from BIOMED-2 protocol primers for framework 2 region (The sample is annotated I5_FR2).

data

AIRR

antibody

Infers V-D-J haplotypes and gene deletions from AIRR-seq data for Ig and TR chains,
based on J, D, or V genes as anchor, by adapting a Bayesian framework.
It also calculates a Bayes factor, a number that indicates the certainty level of the inference, for each haplotyped gene.
Citation:
Gidoni, et al (2019) <doi:10.1038/s41467-019-08489-3>.
Peres and Gidoni, et al (2019) <doi:10.1093/bioinformatics/btz481>.

Ayelet Peres

rabhit

Inference Tool for Antibody Haplotype

Moriah Gidoni

Gur Yaari

samples_db function

A <code>data.frame</code> in Change-O format (<a href="https://changeo.readthedocs.io/en/stable/standard.html">https://changeo.readthedocs.io/en/stable/standard.html</a>) containing the following columns:<ul>
<li><code>'SUBJECT'</code>: subject names</li>
<li><code>'V_CALL'</code>: V allele call(s) (in an IMGT format)</li>
<li><code>'D_CALL'</code>: D allele call(s) (in an IMGT format, only for heavy chains)</li>
<li><code>'J_CALL'</code>: J allele call(s) (in an IMGT format)</li>
</ul>

Format

Example IGH human naive b-cell repertiore — samples_db

A <code>data.frame</code> in Change-O format (<a href='https://changeo.readthedocs.io/en/stable/standard.html'>https://changeo.readthedocs.io/en/stable/standard.html</a>) containing the following columns:<ul>
<li><code>'SUBJECT'</code>: subject names</li>
<li><code>'V_CALL'</code>: V allele call(s) (in an IMGT format)</li>
<li><code>'D_CALL'</code>: D allele call(s) (in an IMGT format, only for heavy chains)</li>
<li><code>'J_CALL'</code>: J allele call(s) (in an IMGT format)</li>
</ul>

samples_db: Example IGH human naive b-cell repertiore

Description

Usage

Arguments

Format

References